csh4lmp

A C++ modeling tool for full atomistic modeling of calcium-silicate-hydrates used in the paper "Bridging the gap between NMR measured mean silicate chain length and nano-scale silicate polymorphism of calcium silicate hydrates.," Yuan Chiang, Shu-Wei Chang, Cement and Concrete Research, 140, 106268.

Calcium-silicate-hydrates (C-S-H) is the main binding materials in the cement hydrates. To date, its atomistic configuration remains a conundrum and under extensive discussion. (Qomi et al. Nat. Comm.) (Kumar et al. ACS. JPCC.) The understanding of nanoscale silicate tetrahedral vacancies in C-S-H polymorphs is absent from previous literature and lack a handy tool to build the full atomistic model of C-S-H with tailored compositions. csh4lmp realizes atomic structure modification through removing silciate monoxdide (SiO), appending hydrogen (H), and inserting water molecules (H₂O) based on the anhydrous supercell of Hamid's mineral 11-Å tobermorites.

Yuan Chiang Mar/2019 @ NTUCE

Citing

If you happen to use/adapt this code or the example C-S-H structures provided in this repo, please cite the associated paper: Chiang, Y., & Chang, S. W. Bridging the gap between NMR measured mean silicate chain length and nano-scale silicate polymorphism of calcium silicate hydrates. Cement and Concrete Research, 140, 106268. Or cite by BibTex: BibTex @article{chiang140bridging, title={Bridging the gap between NMR measured mean silicate chain length and nano-scale silicate polymorphism of calcium silicate hydrates}, author={Chiang, Yuan and Chang, Shu-Wei}, journal={Cement and Concrete Research}, volume={140}, pages={106268}, publisher={Elsevier} doi={https://doi.org/10.1016/j.cemconres.2020.106268} }

Nomenclature and color for atoms

| Type | Name | Element | Color | | --- | --- | --- | --- | | 1 | O (oxygen) | oxygen | red | | 2 | Ca (intralayer calcium) | calcium | blue | | 3 | Si (silicon) | silicon | brown | | 4 | H (hydrogen) | hydrogen | white | | 5 | Oh (hydroxyl oxygen) | oxygen | yellow | | 6 | Ow (oxygen in water) | oxygen | cyan | | 7 | Cw (interlayer calcium) | calcium | magenta | | 8 | Hw (hydrogen in water) | hydrogen | white | | 9 | Ob (bridging oxygen) | oxygen | purple |

Build

make make -f Makefile

Command

• I/O : input and output of LAMMPS data file

input < [input file name] output > [output file name] hint (y/n) - add water : add water molecules to current model

-aw add [#] [typeO] [typeH] syntax | definition ------ | ---------- # | addition number of water molecules typeO | added oxygen type typeH | added hydrogen type

• delete water : remove all of water molecules -dw delete [typeO] [typeH] syntax | definition ------ | ---------- typeO | removed oxygen type in water molecules typeH | removed hydrogen type in water molecules

• remove SiO : remove a number of silicate monoxide -s number [typeSi] [#] [BT/PT ratio] syntax | definition ------ | ---------- typeSi | silicon type # | removal number of silicate units α | vacancy ratio of bridging tetrahedra (BT) to pairing tetrahedra (PT)

• add H : append multiple hydrogen to undercoordinated oxygen -h valence (n/#) [typeO] [typeH] [typeO-H] syntax | definition ------ | ---------- n/# | n : append hydrogen to meet electroneutrality / number of appended hydrogen typeO | atom type of oxygen to be bonded typeH | atom type of hydrogen to be added typeO-H | bond type of new bonds between O and H

• delete atom : delete atoms with specific type -d delete atom type [type] syntax | definition ------ | ---------- type | atom type of atoms to be deleted

• delete bond : -d delete bond type [type] syntax | definition ------ | ---------- type | bond type of bonds to be deleted

• change box : -c boundary [pbcx] [pbcy] [pbcz] syntax | definition ------ | ---------- pbcx pbcy pbcz | periodic boundary condition in x y z direction = p (periodic), f (non-periodic)

This command will reset and make the image flag consistent and traslate the atoms whose bonds cross the boundary

License

MIT